Adding registry web service and changes to WStester and JWS2Client code. Bugs in...

[jabaws.git] / webservices / compbio / ws / server / JronnWS.java

diff --git a/webservices/compbio/ws/server/JronnWS.java b/webservices/compbio/ws/server/JronnWS.java
index 13fe708..dc37f3f 100644 (file)
--- a/webservices/compbio/ws/server/JronnWS.java
+++ b/webservices/compbio/ws/server/JronnWS.java
@@ -1,8 +1,6 @@
 package compbio.ws.server;\r
 \r
 import java.io.File;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\r
 import java.util.List;\r
 \r
 import javax.annotation.Resource;\r
@@ -13,10 +11,11 @@ import org.apache.log4j.Logger;
 \r
 import compbio.data.msa.SequenceAnnotation;\r
 import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\r
 import compbio.engine.AsyncExecutor;\r
 import compbio.engine.Configurator;\r
 import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
 import compbio.metadata.ChunkHolder;\r
 import compbio.metadata.JobStatus;\r
 import compbio.metadata.JobSubmissionException;\r
@@ -51,33 +50,40 @@ public class JronnWS implements SequenceAnnotation<Jronn> {
        private static final PresetManager<Jronn> jronnPresets = Util\r
                        .getPresets(Jronn.class);\r
 \r
+       private static final LimitsManager<Jronn> limitMan = compbio.engine.client.Util\r
+                       .getLimits(new Jronn().getType());\r
+\r
        ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)\r
                        throws JobSubmissionException {\r
                Jronn jronn = new Jronn();\r
-               jronn.setInput("fasta.in").setOutput("jronn.out");\r
+               jronn.setInput(SkeletalExecutable.INPUT).setOutput(\r
+                               SkeletalExecutable.OUTPUT);\r
                return Configurator.configureExecutable(jronn, sequences);\r
        }\r
 \r
        @Override\r
-       public HashMap<String, HashSet<Score>> getAnnotation(String jobId)\r
+       public ScoreManager getAnnotation(String jobId)\r
                        throws ResultNotAvailableException {\r
                WSUtil.validateJobId(jobId);\r
                AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
                ConfiguredExecutable<Jronn> jronn = (ConfiguredExecutable<Jronn>) asyncEngine\r
                                .getResults(jobId);\r
-               HashMap<String, HashSet<Score>> mas = jronn.getResults();\r
+               ScoreManager mas = jronn.getResults();\r
                log.trace(jobId + " getConservation : " + mas);\r
                return mas;\r
        }\r
 \r
        @Override\r
        public Limit<Jronn> getLimit(String presetName) {\r
-               return new Jronn().getLimit(presetName);\r
+               if (limitMan == null) {\r
+                       return null;\r
+               }\r
+               return limitMan.getLimitByName(presetName);\r
        }\r
 \r
        @Override\r
        public LimitsManager<Jronn> getLimits() {\r
-               return new Jronn().getLimits();\r
+               return limitMan;\r
        }\r
 \r
        @Override\r